10: Bowser Necklace
In Ocarina of Time (3D and original) going into view mode in front of Malon (located at Lon Lon Ranch) in the past will reveal a necklace with a Bowser Medallion.
9: It's A Secret To Everybody
In A Link Between Worlds, going into a cave in southern Lorule after completing the Thieve's Lair dungeon will yield a short conversation with the Thief Girl. At the end she says it's a secret to everybody, and gives you a silver (100) rupee. This references the original game, when a Moblin gives you 20 rupees.
8: Princess Zelda Recognizes Pokemon?!
If you enter the courtyard of Hyrule Castle in Ocarina of Time wearing the Keaton Mask, Zelda will ask if you're "one of those pocket monsters", before returning to her weird staring position.
7: Happy Mario Salesman
In Majora's Mask, a mask identical to Mario's face is strapped to the back of the Happy Mask Salesman. It is a little creepy, seeing as it has no pupils, but it is definitely a cool find!
6: The Chronicles of Tingle
In the Wind Waker, a story about "A fairy who helped the hero of time by providing him with maps" can be read (in Hylian) on one of the many text covered walls. This is a reference to the Tingle in Majora's Mask.
5: Yoshi's Awakening
The Trendy Game in Link's Awakening has some lame prizes. However, there is a Yoshi doll to be won! Although it has no significance to the game, it is a fun discovery to be made.
4: Hyrule Castle Paintings
In Hyrule Castle Courtyard in Ocarina of Time. There are paintings of Mario on the walls of the castle hallway that can be seen in view mode.
3: Luigi is Real?!
In Ocarina of Time, a protruding wall inscription says "L is Real" as a reference to a phrase used in the Mario games for N64.
2: ZELDA Dungeon (Before It Was Cool)
In the second quest of the original game, the dungeons layouts spell "ZELDA".
1: A Link Between Majora's Mask
In A Link Between Worlds, the bottom right corner of Link's house has Majora's Mask. Nobody knows if this is a correct easter egg, and the mask is a memento from past adventures, or if it is simply a joke hid by the developers. We got an official timeline out of Hyrule Historia, but a link between worlds was not included.